I would just use the person's Mystic Defense, including bonuses from the armor (if any). Unless it's a thread item (in which case the Mystic Defense is part of the item's information), the armor's Mystic Defense isn't going to be higher except in very rare circumstances.

The Spot Armor Flaw Test is made against the highest Mystic Defense of:

1. The target wearing the armor; or,
2. The armor.

As Mataxes noted, most of the time the target wearing the armor will have a higher Mystic Defense. Generally, only thread armor or other magical armor will come anywhere close to a Namegiver's Mystic Defense.

If you are asking whether the test is made against the wearer's base Mystic Defense (only based on Perception, as in Character Creation), that's generally specifically noted in ability descriptions. Spot Armor Flaw doesn't have that noted, so it's against whatever Mystic Defense the target has, including Discipline bonuses, woven threads, spell bonuses, and so on, which may be active at the time.